peptihub：精确注释的癌症相关肽的精选存储库，具有用于肽探索和发现的晚期公用事业
PeptiHub: a curated repository of precisely annotated cancer-related peptides with advanced utilities for peptide exploration and discovery
影响因子:3.60000
分区:生物学4区 / 数学与计算生物学4区
发表日期:2024 Sep 20
作者:
Sara Zareei, Babak Khorsand, Alireza Dantism, Neda Zareei, Fereshteh Asgharzadeh, Shadi Shams Zahraee, Samane Mashreghi Kashan, Shirin Hekmatirad, Shila Amini, Fatemeh Ghasemi, Maryam Moradnia, Atena Vaghf, Anahid Hemmatpour, Hamdam Hourfar, Soudabeh Niknia, Ali Johari, Fatemeh Salimi, Neda Fariborzi, Zohreh Shojaei, Elaheh Asiaei, Hossein Shabani
摘要
Peptihub（https://bioinformaticscollege.ir/peptihub/）是一种精心策划的癌症相关肽（CRP）的存储库，在科学文献中已记录在科学文献中。 Peptihub中包括各种CRP，展示了各种效果和活动。尽管一些肽表现出明显的抗癌功效，但其他肽则没有明显的影响，有些甚至具有替代性的非药物功能，包括药物载体或致癌属性。目前，Peptihub容纳874个CRP，对10个不同的生物类别，26个器官和438个细胞系进行了评估。数据库中的每个条目都伴随着易于访问的3D构象，这些构象是通过实验或通过预测方法获得的。向用户提供了三个提供基本，高级和BLAST序列搜索选项的搜索框架。此外，对肽的精确注释使用户能够根据其特定活动（抗癌，无效，无效的效果，致癌物等）及其有效性（速率和IC50）在癌症条件下，特别是在单个器官中的效果（速率和IC50）探索CRP。这种独特的属性有助于构建强大的培训和测试数据集。此外，Peptihub提供了1141个功能，以方便选择最相关的功能来解决其特定的研究问题。特征包括AAINDEX1（在六个主要子类别中：α倾斜度，β倾向，组成指数，疏水性，物理化学特性和其他特性），氨基酸组成（氨基酸组成和二肽组成）以及分组的氨基酸组成（分组氨基酸组成（分组的氨基酸组成）类别，分组辅助二培养基和组合物组合和组合。这些公用事业不仅加快了基于机器学习的肽设计，还可以促进肽分类。数据库URL：https：//bioinformaticscollege.ir/peptihub/。
Abstract
Peptihub (https://bioinformaticscollege.ir/peptihub/) is a meticulously curated repository of cancer-related peptides (CRPs) that have been documented in scientific literature. A diverse collection of CRPs is included in the PeptiHub, showcasing a spectrum of effects and activities. While some peptides demonstrated significant anticancer efficacy, others exhibited no discernible impact, and some even possessed alternative non-drug functionalities, including drug carrier or carcinogenic attributes. Presently, Peptihub houses 874 CRPs, subjected to evaluation across 10 distinct organism categories, 26 organs, and 438 cell lines. Each entry in the database is accompanied by easily accessible 3D conformations, obtained either experimentally or through predictive methodology. Users are provided with three search frameworks offering basic, advanced, and BLAST sequence search options. Furthermore, precise annotations of peptides enable users to explore CRPs based on their specific activities (anticancer, no effect, insignificant effect, carcinogen, and others) and their effectiveness (rate and IC50) under cancer conditions, specifically within individual organs. This unique property facilitates the construction of robust training and testing datasets. Additionally, PeptiHub offers 1141 features with the convenience of selecting the most pertinent features to address their specific research questions. Features include aaindex1 (in six main subcategories: alpha propensities, beta propensity, composition indices, hydrophobicity, physicochemical properties, and other properties), amino acid composition (Amino acid Composition and Dipeptide Composition), and Grouped Amino Acid Composition (Grouped amino acid composition, Grouped dipeptide composition, and Conjoint triad) categories. These utilities not only speed up machine learning-based peptide design but also facilitate peptide classification. Database URL: https://bioinformaticscollege.ir/peptihub/.